Last of Prototype
by DarkAvenger001
Summary: After the events of Last of Us, Joel and Ellie are living in peace in Jackson County, Wyoming, the home of Joel's brother Tommy, when they are asked to embark on a mission that will throw them back into the flames as the past catches up with them and an ally that comes to their aid.
1. Chapter 1

**A/N: Please remember to review with any comments, question, concerns, or constructive criticism that you might have.**

Chapter 1:

Here We Go Again

"You can't save her. How long before she's ripped apart by a pack of clickers? That is if she hasn't been raped and murdered first," Marlene said, pointing the gun in her hand at Joel.

"That ain't for you to decide," he replied, showing no fear as he held the unconscious Ellie in his arms.

"It's what she'd want," Marlene insisted. Joel looked down and Marlene, thinking he was considering handing her over, pressed forward, "And you know it. Look…" she said, lowering her gun and taking her hand off of the trigger, "You can still do the right thing here. She won't feel anything." She started moving forward to take the girl from his arms.

b*BANG!*/b

Joel woke up with a start. He looked around and found himself back in his room in Jackson County, Wyoming. He rubbed the sleep out of his eyes in an attempt to clear his mind. It had been three months since that day, the day he rescued Ellie from being sacrificed in order to hopefully create the cure for the Cordyceps infection that's ravaged the world. The day has been haunting his dreams ever since he killed Marlene. He didn't know why because he did it to protect Ellie and give her a chance at life. He was snapped out of his thoughts by someone knocking on his bedroom door.

He pulled on some pants and a shirt before shouting, "Yeah!?"

The door opened to reveal Ellie, the auburn-haired fourteen-year-old that Joel protected from Boston to Salt Lake City. She doesn't know the truth about what happened back in Salt Lake City, but Joel often worries that she suspects there's more than what he told her.

"Joel, Tommy's here. He wants to talk to you."

"Thanks, Ellie," Joel said, as he walked out to the front door where his brother Tommy was waiting. "What's going on, Tommy?"

"I was hoping you could help me with a little something," the unofficial leader of the county said, "We found a hidden military base and I was hoping you'd go with the team. I need the best people on the team and you're one of the best that I know."

"Alright, let us just go grab our gear and we'll meet the team."

"We?"

"Ellie's coming too," Joel said, heading back to his room to pick up his pack where his weapons and supplies were stored.

"You sure?" Tommy asked, looking at the fourteen year old, who was following Joel down the hall to her own room.

"She's been through worse. Besides, she'd come whether or not we brought her along, right, Ellie?"

"Fuck yeah, I would!" Ellie said, grabbing her own pack.

Tommy wasn't completely sold on the idea of Ellie joining the team, but figured there wasn't anything he could do to change either of their minds, due to both being well-known for their stubbornness.

"Alright," Tommy said, "Meet them at the front gate. Amir knows the way and he'll lead the way." With that, Tommy left the house to do some other business that required his attention.

Ellie and Joel made their way to the front gate after getting their packs and found their team of three others, Amir, another man named Steve, and a woman named Hannah.

"Didn't know this was gonna be a babysitting mission too," Steve said, his dislike of Ellie's presence being completely obvious, much to the annoyance of the girl.

"Hey, fuck you, man! I can take care of myself!" Ellie replied.

"Sure you can," Steve said smirking

"Can we get on with this already?" Joel asked.

"Yeah, come on, Steve, we've got a job to do," Amir said, leading the group out, "Okay, the base we're going to is a couple hours away by foot."

"If it's so close, why's it taken this long to find it?" Hannah asked.

"Apparently, it was being kept hidden for some reason. So much so that even before the world went to shit it couldn't easily be found unless you knew it was there. The way there seems to be free of clickers."

"What about inside?" Joel asked.

"Unknown, but it looks like the place hasn't been looted yet, so we could find weapons, medicine, food, who knows what else," Amir said.

"Fuck, how did we find this place?" Ellie asked.

"Old records, rumors, and a lot of luck," Amir replied.

The rest of the trip was done in relative silence until they reached an automatic gate. It was blocked off from the other side and the top was blocked off with barbed wire.

"Shit, we gotta find some way in," Amir said, looking around.

Joel and Ellie started walking around the right side of the fence, while Hannah and Steve took the left with Amir waiting back at the gate to watch if any clickers showed up. Joel and Ellie found a hole at the bottom of one section of fence. Ellie, having done it many times before, crawled through and started making her way to the gate. Joel used the walkie talkie he had on his pack to call the others, telling them what they were doing and to meet him at the gate.

Ellie unblocked the gate and opened it up, smirking at Steve, "Still think I need babysitting?"

"Guess you've got some use," Steve said, walking past her.

"Nice one, Ellie," Joel said, giving her a pat on the shoulder.

"Thanks, Joel," Ellie said smiling.

The large metal door to get into the base was ajar so the group got inside relatively easily. There were still emergency lights, which didn't really surprise anyone as the generators in charge of such things were typically built to last. They moved as silently as they could in an attempt to avoid the attention of any infected within the base. Moving through one of the main halls, Ellie made a discovery on one of the walls.

"Hey, look at this," she whispered, her flashlight illuminating a map of the base.

The others crowded around, stealing glances around to make certain nothing was creeping up on them in the dark.

"Here," Amir said, pointing at the area of the map marked 'medical facility,' "If there's medicine anywhere, it'll be here. Steve and Hannah will go there and grab the medical supplies. I'll head to the armory marked on the map and grab what I can there. Joel, Ellie, I want you two to head to the mess hall and gather any unspoiled food that you can. We'll meet back here," he said, pointing to a large room the map showed was connected to the place marked as 'vehicle bay.'

Joel and Ellie took the hallway that would lead them to the mess hall. There were still no clickers to be found. That changed when they opened the door to the mess hall. As soon as the door was open a crack, they heard the telltale sounds of clickers. They immediately crouched down and slowly entered. There were three clickers just milling around. Joel moved up behind one and stabbed it in the neck with one of his homemade shivs. He repeated this with the second one, but when he attempted to do the same with the third, he accidently knocked a glass bottle off the table, causing it to smash against the floor and alerting the clicker.

"Shit!" Joel said as it shrieked and charged him.

Ellie jumped on its back and stabbed it repeatedly in the head with her switch-knife, killing it.

"Thanks, Ellie," Joel said.

"You're welcome," the girl said before they started searching through the kitchen, looking for any food they could still eat. They found a few MREs, some canned food, and a couple unsquished twinkies.

"Looks like that's all we'll find here," Joel said, "We better head back."

"Right behind you," Ellie assured him.

The two made their way back down the hall and went to where they were supposed to meet the rest of the group. Amir was already there, his pack heavy with ammo and extra weapons, and Hannah and Steve arrived a few minutes later.

"Any luck?" Amir asked.

"Not much in the way of food, but we managed to find some stuff we can use," Joel said.

"We pretty much drained the clinic dry of medicine and other stuff," Steve said, gesturing to his pack.

"Good, let's move," Amir said as he opened the door they headed through the hall to the vehicle bay.

When they headed into the vehicle bay, they found that going inside was a mistake as the sound of the squeaky door alerted the not one, not two, but three bloaters to their presence. The massive infected roared and began to lumber towards the group.

"Shit, run!" Amir yelled as they ran back the way they came, hoping to outrun the massive infected.

Two of the three hallways that were now blocked by clickers that heard the bloaters' roars and came to seek the source of the noise. The group ran down the third with Joel and Ellie being the last two in the line. About twenty feet down the hall, a clicker burst out of a side door and grabbed Hannah before sinking its teeth into her neck. She only had time to scream once before her throat was ripped out. Knowing they couldn't afford to slow down, the two took the door and kept running as fast as they could. They quickly found themselves in a dead end with a heavy locked door being the only way to go.

"Fuck! What'll we do, Joel?" Ellie asked, panicking as the infected started moving down the hall.

"Try in here!" Joel said as he began slamming against the door. It wouldn't budge from his slams and the infected were getting closer and closer until Joel finally broke through, "Inside!" he ordered and the two piled into the room before they slammed the door closed and blocked it off. A few seconds later, the infected started banging on the door.

"Fuck, what'll we do now?" Ellie asked.

"I don't know," Joel replied after a quick scan around the room.

It was a lab of some kind judging from the advanced technology filling the room. One of which seemed to be a big metal tube with a small window in it. From what Joel could see, there wasn't another way out.

"Hey, Joel, unexcavated means that it wasn't dug out, right?" Ellie asked suddenly.

"Yeah, it's usually for when people build a building around bedrock or something. Why do you ask?" Joel asked, glancing through some papers that had been left abandoned in the room. They were filled with scientific terms and methods that he couldn't even begin to follow.

"That map we looked at earlier said that this area was unexcavated. Why would they say something wasn't built if there was a room here?"

"Either the map was out of date or they didn't want someone to stumble on this room by accident."

"Why? It doesn't look like there's anything interesting here," Ellie said, moving over to the tube.

"Do I look like a scientist? I can't make heads or tails out of these notes," Joel said, tossing the papers back down.

Ellie pulled herself up to peer into the window on the tube. What she saw startled her enough that she dropped back to the floor with a yell of "Fuck!"

"What is it?" Joel asked, rushing to her side.

"Th-there's a person in that thing!"

"What?" Joel asked, moving to look himself. Sure enough, there was a man in a hospital gown in the tube. He had short black hair and Caucasian skin. It looked like he was frozen solid. "What the hell?"

"Sh-should we get him out of there?" Ellie asked.

"It's not our problem. We don't have time to waste trying to let him out. We've got to find a way out of here."

"But, Joel, he might know a way out that we don't!"

Joel sighed and moved to the console nearest to the tube. He started pressing random buttons, trying to get something to happen. It was a few minutes before he managed to get a message that said "UNFREEZING PROCESS COMMENCING." The process took a few seconds before the tube opened with a hiss and the man inside dropped hard to the ground. After a few seconds, the man groaned and coughed a little before he rolled onto his back. He blinked a couple of times to clear his eyes and looked at Ellie who was standing over him.

"Aren't you a little short for a stormtrooper?" the man groaned, making Ellie look at Joel in confusion, but the elder man waved it off. The unfrozen man stood up and looked at Joel, then Ellie, and then back at Joel, "Aren't you Blackwatch guys recruiting a little young? What is this, 'bring your daughter to work' day?"

"Blackwatch? Who's that?" Joel asked.

"Uh, the owners of the base you're in. How could you not know?" the man asked, thoroughly confused.

"This place has been abandoned since the outbreak. We had no idea who ran this place," Joel said.

"Outbreak? They haven't wiped out the Mercer virus?" the man asked, "What year is it anyway?"

"It's 2034," Joel said, much to the unfrozen man's shock.

"What the fuck!? I was in there for over twenty fucking years!?"

"Keep quiet," Joel ordered, "The outbreak we're talking about is the Cordyceps infection. It's caused people infected with it to become what we call clickers and try to kill or infect the healthy."

"Uh huh," the man said, looking at the blocked door, "Why is the door blocked off?"

"There's a bunch of clickers outside and we were hoping you'd know another way," Ellie said.

The man smirked, "You two have no idea what the Mercer Virus does to people, do you?"

Ellie shook her head and Joel said, "Just that it turns them into monsters."

"A crude, but accurate description," the man said moving over to the door before moving the barricade. He looked back at the two. "You may want to stay back." The two people stood back as the unfrozen man pulled the barricade out of the way and opened the door. One of the clickers burst into the room, but the man hit him with a frontal kick with the force of a wrecking ball. It splattered against the wall on the opposite side of the hall from the door. A second tried to attack him but he punched straight through its chest. The man turned back to the two others, "Oh, I forgot to introduce myself. I'm Alan Cogburn Thompson," he said as he bowed to the two, seemingly not noticing the third clicker that was coming up behind him. When it got within grabbing range, Alan's hands turned into massive claws and sliced the clicker in half.

"What the hell are you?" Joel asked, drawing his pistol and aiming it at Alan.

"I'm infected with the Mercer virus," Alan said, "It turned me into a living virus, giving me all sorts of unusual powers. Unfortunately, I was captured by Blackwatch and brought here. Don't worry though, I'm not contagious."

Joel kept the gun pointed at him for a few more seconds before lowering it, "Alright, I'm Joel, this is Ellie. Why don't you lead the way?"

"Better not try and mess with us or we'll fuck you up," Ellie said.

"I'll be sure to remember that, baby sister," Alan said, smirking as he grabbed some of the papers to look at a later time. He used his powers to make his body change the clothes he was wearing to a dark grey hoodie, a black leather jacket, black jeans, and black boots. His arms also turned back to normal.

"Whoa, that's awesome," Ellie said at the demonstration of his abilities.

"Thanks, baby sister."

Joel contacted the others through the radio. Amir and Steve were all right and could get back to the meeting point if the bloaters could be eliminated. Alan shrugged when Joel looked at him questioning. Since he didn't know what bloaters were, he figured he'd give it a shot. They found their way back to the meeting point. The bloaters shot their balls of caustic spores at the three, but Alan pushed the two humans back through the door and shut it, taking the full brunt of the attack.

Alan hacked and coughed upon inhaling the spores, something about them affecting even his blacklight-powered body. Shaking it off, Alan charged at the massive fungal infected, his claws brought to bear. He cut the head off one and drove his claws into the gut of another, eviscerating it. The third managed to grab Alan, picking him up off his feet by grabbing his arms with its thick hands. It bit into Alan's shoulder, making him cry out in pain. Fighting through the pain, Alan tried to find enough leverage to use his claws, but couldn't break free. The bloater had enough strength to keep him from breaking free. Its grip was broken when Joel came back in the room and shot it in the head with his hunting rifle. Alan dropped to his feet and decapitated the bloater before tendrils came out of his body and absorbed the massive creature.

Rather than feel regenerated like he expected, it suddenly felt like his entire body was on fire and he should know considering he was once lit on fire. He dropped to his knees and wrapped his arms around his body as if to smother the invisible flames. The tendrils that made up his body began to writhe as it fought off the effects of the fungal infection.

"What's the matter?" Joel asked keeping Ellie from getting too close.

"I, ugh, don't know. This has never, unh, happened before," Alan said, getting back to his feet, the pain finally subsiding and his wound healed itself, "Guess the Cordyceps and the Mercer virus don't react well together."

"How did you do that absorbing thing?" Ellie asked.

"It's called consumption. It's not so much eating as the name makes it sound, but rather like how some one-celled organisms absorb other such organisms. When I do it, I gain the abilities, skills, and memories of the target, assuming they were killed recently. I'll even gain the ability to transform into the person that I absorb."

"Cool, sick, but cool," Ellie said.

Just then, Amir and Steve arrived and their eyes immediately went to Alan.

"Who's this?" Amir asked, distrustful of the new face.

"Name's Alan. I was, uh, living in here until I found Ellie and Joel. I helped 'em out and they invited me back."

"Fine," he said, not entirely buying the story, but accepting it. He led the group to the vehicle bay where they managed to find a van with gas and the keys nearby. They took it and drove back to Jackson County, not knowing that the releasing of Alan activated a silent alarm.

Meanwhile, in the ruins of New York City, a man was rushing through a military base, searching for someone.

"Sir! Sir!" he called, seeing his commanding officer.

"What is it, Sergeant?" the man asked looking up from the reports he was reading.

"Do you remember that alert report that you told us to watch out for?" the first man asked, "The one in Wyoming?"

"Yes, what about it?" the officer asked.

"It's gone off."

That got the officer's full attention, "Scramble all troops! We need to head to Wyoming now!"

"Yes sir!" the man shouted running off to do his orders.

"If we don't hurry, what little order we've been able to put into place will be destroyed," the officer said, muttering to himself.

Back in Wyoming, Joel's group was still driving and just came over a ridge to see a sight that chilled their blood.

"What the hell?" Joel asked.

"I'm guessing it doesn't usually look like that," Alan said.

Jackson County was in flames.

**A/N: And there's chapter 1! Please remember to review with any comments, question, concerns, or constructive criticism that you might have.**


	2. Chapter 2

**Reviews:**

**coduss**

**Glad you like it. Hope you continue to do so.**

**Bgrim8633:**

**Happy to hear that. I hope it lives up to your expectations.**

**gamerAssassin:**

**I agree. I played them so many times that I could probably quote each line from memory.**

**A/N: Please remember to review with any comments, question, concerns, or constructive criticism that you might have.**

Chapter 2:

Joel's Past Catches Up

After the group experienced the horrifying sight of their home drowning in a sea of flames, they abandoned their car and started towards the walls on foot to hopefully remain undetected by whoever attacked it. Alan took the lead with Joel and Amir behind him to his left and right respectively. Ellie stood between them and Steve brought up the rear. They managed to make it to the wall without being spotted and found a hole blown in the defenses. They took cover against buildings just before they came to the first open area. Alan used his powers to activate his thermal vision and spotted one man in the area. Judging from the fact that he wasn't rushing to help put out the fires and that he was surrounded by corpses, Alan figured he was one of the invaders.

"Wait here," Alan whispered as he moved out from cover to make his way to the guy while he had his back to the stalking infected. Alan put the man in a headlock, making his chin touch his chest, before pushing more on his head, snapping his neck and consuming him. He took the dead man's form and walked back to his team.

"W-what the fuck? H-how did you do that?" Amir asked.

"Let's just say that I've got some very…unique abilities. One of which involves absorbing a person and gaining his form, memories, and skills," Alan said.

"So what'd ya learn?" Ellie asked as Alan changed back to his original form.

"He was a part of some group called the 'Fireflies.' Does that mean anything to any of you?" Everyone's eyes widened in shock, "I'm guessing that's a yes," Alan said.

"Yeah, Tommy used to be a member of their group, but left years ago!" Amir said.

"We've got some history with them, too," Ellie said, "But none of it really explains why they're attacking us."

"That guy didn't really know most of the details. He just knew that they were looking for someone that their leader will be able to recognize. He didn't know the person's name, just that he supposedly took something that was said to be the 'last hope for humanity,'" Alan said, "The leader's words, not his."

Alan noticed a slight grimace from Joel when he said this, but it was only there for a second and no one else seemed to notice. Ellie, however, shot Joel a questioning look. The blacklight infected figured he'd ask about it later, since he was clearly missing something.

"So, where are the rest of them?" Steve asked, looking suspicious at Alan, as well as the two newest members of the community, Joel and Ellie.

Alan pointed down the road, "They're all that way, holding the hostages including the leader of this place."

"They have Tommy?" Joel asked, worried.

"Yeah, it appears they want him to tell them where the one they're looking for is hiding the thing he stole, whatever it is."

"We gotta save him!" Ellie insisted, despite no one arguing the fact.

It was decided that Alan, in the form of the deceased Firefly, would walk down the road while Joel and Ellie would take a path through the buildings to the left while Amir and Steve did the same to the right. Joel was moving as silently as he could with Ellie staying right behind him. They found a couple of Fireflies watching from inside one of the houses they passed through. Joel strangled one of them while Ellie jumped on the back of the other to stab his chest several times with her butterfly knife. They managed to reach the center of town without being spotted, but after that, things got more difficult.

Tommy was kneeling in the middle of the large square, his arms tied behind his back, with his now pregnant wife, Maria, along with three others, all in the same condition. One of the Fireflies, a larger man with a scar that went from his top lip to his chin, was standing in front of Tommy, yelling at him. The humans in Alan's group made their way into buildings, taking out the snipers guarding the area and taking their rifles. Alan, in his Firefly disguise, made his way closer to where the hostages were being held.

As he got closer, he could make out the words of the leader, "…ell are they!?"

"I told you already! They left months ago!" Tommy said.

The leader pistolwhipped him, cutting his lip and making Tommy spit out some blood, "Don't fucking lie to me! I know they were seen here just this morning!"

"I don't know where you heard that, but it's wrong! They're long gone!" Tommy insisted.

"Alright, if that's the way you want to play it," the leader said before he moved his gun and killed one of the hostages with a single shot to the head. The hostages howled in anger and horror at the cruelty.

"Damn you, you bastard!" Tommy roared, his face contorted in an expression of rage.

"Stop wasting my time and tell me where they are!" the Firefly leader demanded, turning his aim to Maria.

Just then, one of the Fireflies guarding the area noticed the advancing disguised Alan and approached him.

"Hey, Mac, what are you doing here? I thought you were holding the perimeter down the wall," the guard said.

Alan spoke in the consumed man's voice, "Yeah, the others sent me up here to talk to the boss."

The man looked suspicious at that, "Why didn't you just use the radio?"

Alan glanced past the man blocking his path and saw that the leader was preparing to execute the pregnant woman. He knew that he couldn't afford to waste time, so he said, "Ah, fuck it," before driving his fist through his chest. He changed his hands into claws and sliced the head off of another. Joel and the others opened fire on the other guards while Alan leapt at the leader, who rolled back to dodge the attack.

He fired his pistol at Alan, who took the shots, but healed seconds afterwards. The Firefly leader dodged each of the wild attacks Alan sent his way. He rolled back and snatched up a grenade launcher one of the fallen Fireflies dropped before rolling onto his back as Alan launched himself at him again. The leader fired a single shot at the attacking Evolved, hitting him square in the chest with the shot and sending him flying into one of the buildings.

"Fall back!" the Firefly leader ordered as the remaining Fireflies fled the town, but not before he locked eyes with Joel.

As the last of the Fireflies fled, Alan walked out of the rubble of the house he'd been blasted into, dusting off his shoulders, his wound fully healed. He walked over to the hostages before using his claws to cut their binds. As soon as they were freed, Tommy and Maria embraced one another, each glad the other was safe. Joel and the others approached them and Tommy helped his wife up before starting to give the different people orders.

"Amir, you and Jack, go searching for other people to take care of the wounded and anyone else that might need help. Steve and Damian, go gather any of our forces and make sure no clickers managed to sneak in while this shit was going down. Ellie, could you take Maria home for me?"

"Sure thing, Tommy," Ellie said, as she and the pregnant woman headed out to go to Tommy's house.

Once they were out of earshot, Tommy turned to Alan and Joel, "You two need to start explaining a few things. Let's start with how the hell you are able to survive a direct hit from a fucking grenade launcher, not to mention that shapeshifting shit you did," he said to Alan.

"Heh, funny story about that," Alan said before explaining precisely what he was in terms of his powers and origins.

"So, let me get this straight, you're infected by that big, nasty virus back from the New York quarantine and Joel just brought you here?"

"He proved that he was trustworthy, Tommy," Joel said, "He helped us out in the base. Without him, I'm not sure we would have made it."

"Alright, I can accept that, especially since he helped save Maria. Now, would you mind explaining why exactly the Fireflies are so hell-bent on finding you and Ellie?" Tommy demanded.

"That's a bit of a long story," Joel said, waving off his question.

"That's not good enough, Joel," Tommy said, "Not now that they've attacked our home, so start talking."

Joel looked at Alan, hoping to get him to leave so he could speak to Tommy alone, but it was clear that Alan wasn't going anywhere, wanting to hear the story behind these so-called 'Fireflies.'

"Alright, fine. Well, Ellie and I did meet the Fireflies like I said we did, but unlike what I told you, where they had already tried to cure the disease with other people like Ellie, it went completely different. They sedated her and were planning to carve her brain apart to get the cure. They were going to **kill** her! They didn't even give her the chance to say what she wanted. I couldn't let that happen, so I broke her out, despite the Fireflies doing everything they could to stop me."

"What did you do?" Tommy asked, getting a sinking feeling.

"I killed them. In order to save Ellie, I killed the guards, the doctors, and when she tried to stop me, I killed Marlene too," Joel said, his tone daring Tommy to argue against his choices.

"Jesus, Joel, you killed the fucking leader of the Fireflies!?" Tommy questioned.

"Don't start with me, Tommy," Joel warned, "You can't honestly say that you would have let them just kill her either."

Tommy sighed, "You're right, but you still should have told me. Now when people find out about this, especially since Damian, the town blabbermouth, knows they were looking for you and Ellie, they're probably going to come to me to decide what to do with you two."

Joel nodded, having anticipated this already and knowing that these problems would come, which is why he didn't tell his younger brother.

"I'll do what I can for you, but it might be best if you and Ellie stayed out of sight for a while," Tommy said, before going off to deal with the problems.

Joel looked at Alan, who had an intrigued expression on his face.

"What?" the elderly survivor asked.

"It just seems to me like people are making a big deal out of you refusing to sacrifice your daughter," the Evolved said.

"Ellie's not my daughter."

"You both act like it," Alan said, simply, as he started going through the pockets of the dead Fireflies.

"Yeah, I guess we do. It's just I look out for her; take care of her, you know," Joel said.

"Fair enough," Alan said, "She seems to look up to ya, so be careful," he warned before finding something in one of the corpses' pockets, "Hey, nice iPod and it still works!"

Joel smirked at his sudden change from being serious to focusing on the iPod, "Hey, why don't you come to our house? We don't exactly have another bed, but the couch is comfortable enough."

"That's mighty nice of you, Joel," Alan said, before they headed to Joel and Ellie's home.

About five minutes later, Ellie was heading back to the house that she shared with Joel. Despite trying to keep it hidden, Ellie was pissed. First at the Fireflies who were supposed to be the good guys, not raiders that attack innocent settlements! Secondly and mostly at Joel, who Ellie could tell that he had something to do with the Firefly attack. She knew from arriving in Jackson County after the Fireflies, according to Joel, told him they gave up on searching for the cure that Joel had been hiding something, but she'd never considered it'd be bad enough for the Fireflies to actually do something like this. Well, she wasn't going to let this continue. Joel was going to tell her everything!

When she got back to the house, she entered to find her new acquaintance, Alan, lying back on the couch, staring at some papers she'd seen him grab from the Blackwatch base and listening to a device she saw in an old magazine once.

He was singing quietly, "There's a fire inside heeeerrr and it's made her a fiiiighteeerrr. I will let the world burn if it means I'll survive, but the thing I put first is the girl by my side." (A/N: If you're interested, this song is 'A Reason to Live' by JTMachinima. Just search youtube for it.)

Ellie smacked his foot, getting his attention away from the papers.

"Well, hello, there baby sister!" Alan said, moving his feet to let Ellie sit next to him.

She looked over at the papers Alan was looking at, "So, what are these anyway?"

"They appear to be the results of some experiments involving this Cordyceps infection. It looks like they were examining it to see if it could work as a counteragent for the Blacklight virus," Alan said just as Joel came into the room.

"You can actually understand that scientific mumbo jumbo?" Joel asked.

"Well, you eat enough Blackwatch scientists, you tend to learn a thing or two," Alan said, laughing internally at the two's slightly pale faces.

"So, uh, did you learn anything?" Ellie asked.

"Well, for one thing, it appears that the scientists were experimenting on the original strain," Alan said.

"What does that mean?" Joel asked, thoroughly confused.

"Well, it either means that either Blackwatch managed to get a sample at the earliest stages of the infection or… well, the second option is a bit more disturbing."

"Says the guy that eats people," Ellie said, making Alan chuckle, "What's the second option?"

"Well, the Cordyceps fungus has always existed, but it used to only affect insects. We know that it spontaneously did a species jump to infect humans. The second option would be that the species jump wasn't natural and that someone intentionally caused it."

"Why would someone do that?" Joel asked.

"Bio-weapon maybe. I'm sure there are other reasons, but I can't think of them. Regardless, that's not the interesting part."

"What's the interesting part?" Ellie asked.

"The dates on these reports. They're dated two years before the infection broke out."

"What does that mean?" Ellie asked. Joel's face told Alan that he knew what it meant.

"Well, baby sister, it means that the government knew about the infection before it spread across the world and didn't tell anyone, so either they thought it was contained or the government created it," Alan said.

"Shit," Ellie said in horror at the prospect. Sure, the government worked to train her when she was in the orphanage and they weren't exactly known for their subtlety or moderation, but still the idea that they were the cause of all of this was too much. Just when she accepted the idea, Ellie turned to Alan, "Hey, would you mind giving me and Joel a few minutes?"

"Sure thing, baby sister," Alan said as he decided to go for a walk.

Once he left the house, Ellie turned to her guardian, "Okay, Joel, start talking. Why are the Fireflies coming after us?"

"Look, Ellie, I don-"

"No, Joel. No. No more lies. No more secrets," Ellie said, "Tell me everything and I mean, **everything**."

Joel sighed and told her everything that had transpired between him and the Fireflies ending in the death of Marlene, the woman that had looked out for Ellie until she left the girl in Joel's care. Ellie wasn't happy.

"What the fuck, Joel!?" she shouted pushing him. "How could you not tell me this? Why the fuck did you lie to me?"

"I wanted you to remember your friend Marlene as she was before she tried to…do what she did," Joel said.

"Bullshit! I told you no more lying! You were worried that I'd suddenly get suicidal and let the Fireflies cut me up!"

"Maybe so. I was worried about losing you. I've lost a lot, you know that, and I couldn't just risk losing someone else."

"That's not the point, Joel. It should have been b my/b choice, not yours."

"Ellie, the Fireflies weren't going to give you a choice, so I made it for you," Joel said, making Ellie calm down a little.

"Alright, just no more lying from now on," Ellie said before heading to her room, leaving Joel to think on that.

While Joel and Ellie were talking, Tommy was having to deal with certain members of the community as they got word of what it was the Fireflies were looking for when they attacked, or rather **who** it was.

"Tommy, we need to get them out of here. Having those two here brings danger to all of us!" Steve said as other members nodded their agreement.

"We can't just throw them to the wolves, Steve," Tommy replied, "They've proven themselves to helpful to the community. We should show a little gratitude for all they've done."

"Look, Tommy, you're right, sure, and I get he's your brother, but if it were anyone else, would you really be considering this?" Steve asked.

"Of course I would. You're talking about tossing people out on their asses when they've got people hunting them!" Tommy said.

"Yeah, I get that, but those same people just broke down our door and nearly wiped us out. If they're still here the next time, what's to stop the Fireflies from wiping us out?"

Tommy sighed. This was going to be a long night.

A couple hours later, Joel, Ellie, and Alan were sitting at what passed for their dinner table, enjoying a bit of dinner, though Alan, as a living virus, didn't eat.

"Hey, Alan, why do you call me 'baby sister?'" Ellie asked.

"Same reason my middle name's really Cogburn. My dad was a big John Wayne fan and he pretty much raised me on the Duke's works."

"The Duke?" Ellie asked, not knowing who Alan was referring to.

Alan gave Joel a look as if to ask if she was serious and received a nod in response.

"That's just a real tragedy," Alan said, shaking his head in disappointment, "The Duke, John Wayne, was an actor, one of the best in my opinion."

"Guess I'll never get to see any of his stuff."

"Never say never, baby sister," Alan said, smirking, "You never know what can happen after all."

Just then, someone knocked on the door and Alan answered it to find Tommy, who had a very serious expression on his face. Alan let him in and he made his way to where Joel and Ellie were.

"Tommy? What is it?" Joel asked.

"I'm sorry, Joel. I did what I could," Tommy said, his face one of deep depression and failure.

"What happened?" Ellie asked, as Joel got a sinking feeling in his gut.

"They're kicking you three out. There's nothing more I can do," Tommy said, "I'm sorry."

"How long do we have?" Joel asked.

"Twenty-four hours. You can take supplies, weapons, and a car, but you have to be gone in twenty-four hours."

"But, where will we go?" Ellie asked.

"I think I've got an answer for that," Alan said, "You could come with me."

"Where are you going?" Joel asked.

"Where I can hopefully find more information on what Blackwatch was up to; the place where I know they, at least at one point, had a presence: the city that never sleeps, New York City," Alan said.

**A/N: Please remember to review with any comments, question, concerns, or constructive criticism that you might have.**


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